Re: problem with PyNIO dimension sizes

Hi Zach,

Yes it does appear that something is not working right when some of
the dimensions have single elements. However, for what I think you
are trying to do there is a work-around. The code you posted and as
edited by Mary below has some problems. First of all, you can only
create a dimension or a variable in a file once, so you are sure to
get an exception the second time through the loop. Second you are
creating the level dimension with 1 element, yet your use of the loop
counter t suggests that you really mean it to have 'nt' elements.

Assuming this is your intention, it should work with the following
modifications:

import numpy
import Nio
import os
ncols = 1024
nrows = 1024
nt = 41

# Ingest data
#databin = array.array('f')
#databin.read(fileobj, nt*nrows*ncols)
#prcp = numpy.array(databin, dtype='float32')
prcp = numpy.zeros(nt*nrows*ncols,dtype='float32')
prcp = prcp.reshape(nt,nrows,ncols)

os.system("rm -f test.nc")
ncfile = Nio.open_file("test.nc","c")

ncfile.create_dimension('x',ncols)
ncfile.create_dimension('y',nrows)
ncfile.create_dimension('levels',nt) ###
ncfile.create_dimension('record',1)

d4 = ('record','levels','y','x')

prcp_NC = ncfile.create_variable('prcp','f',d4)

# either of the following work for me (using PyNIO 1.3.0b1)

for t in range(nt):
         prcp_NC[0,t,:,:] = prcp[t,:,:]

# or most simply

prcp_NC[:] = prcp[:]

---------

However, note that if the level dimension 'nt' is actually equal to
1, then neither of the methods work. This is definitely a bug and
will be addressed as soon as possible.
   -dave

On Dec 12, 2008, at 3:25 PM, Mary Haley wrote:

> Hi Zach,
>
> This looks like a bug, but I'm not certain.
>
> I took your code snippet, and made it into code I could actually
> run, and I got the same results as you:
>
> import numpy, os, Nio
>
> ncols = 1024
> nrows = 1024
> nt = 41
>
> prcp = numpy.zeros([nt,nrows,ncols], dtype='float32')
>
> filename = "test.nc"
>
> for t in range(nt):
> if os.path.exists(filename): os.remove(filename)
> ncfile = Nio.open_file(filename, 'c')
> ncfile.create_dimension('x',ncols)
> ncfile.create_dimension('y',nrows)
> ncfile.create_dimension('levels',1)
> ncfile.create_dimension('record',1)
> d4 = ('record','levels','y','x')
> prcp_NC = ncfile.create_variable('prcp','f',d4)
> print prcp_NC.shape
> print prcp.shape
> print prcp_NC[0,0,:,:].shape
> print prcp[t,:,:].shape
> prcp_NC[0,0,:,:] = prcp[t,:,:]
>
> Hopefully Dave can take a look at this and see a work-around. I
> tried a few things with no luck.
>
> --Mary
>
> On Fri, 12 Dec 2008 10:48:16 -0600
> Zach DuFran <zdufran_at_wdtinc.com> wrote:
>> I am trying to write a 4D variable to a NetCDF file and I am
>> receiving a fatal error. The line where the error occurs is
>> prcp_NC[0,0,:,:] = prcp[t,:,:]. I have printed out the shapes of
>> each variable and they match. When I switch the order in prcp_NC
>> to be prcp_NC[:,:,0,0] the script will run succesfully, but the
>> data in the NetCDF file is all blank.
>> If I assign prcp_NC as a 2D variable (only x and y) and do prcp_NC
>> [:,:] = prcp[t,:,:] the data is written correctly.
>> The error message for the attached script is:
>> fatal:Dimension sizes of left hand side do not match
>> right hand side
>> The only way I can get the assignment to a 4D variable to work is
>> to add 2 loops so the code reads:
>> for i in xrange(nrows):
>> for j in xrange(ncols):
>> prcp_NC[0,0,i,j] = prcp[t,i,j]
>> Of course, this method is considerably slower.
>> I would appreciate any help you can provide-
>> Zach DuFran
>
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Received on Sun Dec 14 2008 - 13:13:18 MST